Commenting MyGraph.java - You should fill out the comments of MyGraph to be complete. The method comments that are there are fine to leave there, but you should also feel free to rewrite them if you'd like - add or remove stuff. But you should add a file header and comments internal to your methods. In addition please comment any extra methods you write. Basically feel free to use what is there as far as comments go - don't feel that you must re-write them, but add other comments as needed.
Commenting Other files - You do not need to comment Vertex.java or Edge.java unless you add something new to those files. If you do add something, you should comment it. You do not need to add comments to Paths.java. It was written without comments to force you to have practice with reading thru someone else's code. You do not need to add comments to it - but it is fine if you do. You should not be changing Graphs.java at all, you do not need to comment this file.